The wreckage of a Boeing 727, which was believed to have been carrying up to 10 tonnes of cocaine when it crashed in the Malian desert. Photograph: Serge Daniel/AFP/Getty Images

As the daily power cut struck Timbuktu, the town and surrounding desert were plunged into a sandy, grey darkness. Mohamed – a 31-year-old native of the town dressed in rich, deep blue cloth that engulfed his head in the traditional Tuareg style – seemed to shrink further into the shadows. He tipped ash into a saucer as he talked and smoked, telling his story for the first time.

"I didn't know cigarette trafficking was illegal," he said, exhaling into the black. "I smoke, everyone here smokes, so it didn't seem serious. But when I started transporting cocaine … I'm a Muslim, I knew it was wrong."

In 2009 Mohamed, who spoke to the Guardian on condition of anonymity, joined a team that drove packages of cocaine across the Sahara. He and his boss – who introduced him to the illicit trade in cigarettes as a young apprentice – were lured into the business by the apparent wealth of Moroccan and Algerian narco-traffickers whom they encountered in desert towns.

"When we transported cigarettes, I would be paid around 100,000 CFA francs [about £130] for each trip. With cocaine, I earned 1 million," Mohamed explained. "We would drive through the desert in convoys, and each car would earn roughly 18m CFA – the driver, security man and I would all be paid a fee, and my boss would keep the rest."

It is impossible to estimate how many young Malians are, like Mohamed, drawn into drug trafficking by the prospect of earning big money in short periods. In a region where youth unemployment and poverty are high, the prospect of travelling for days at a time through one of the most inhospitable terrains on earth offers little deterrent.

"It was hard, but there was no other way I could earn that kind of money," said Mohamed. "Our routes were never fixed, but we would drive 24 hours a day, without stopping, until we got there. We would eat tinned food, and prepare tea in the car. The most important thing was to get there as quickly as possible."

The UN estimates about 18 tonnes of cocaine, with an estimated street value of $1.25bn (£800m), crosses West Africa every year – nearly 50% of all non-US-bound cocaine. Most of it originates in Colombia, Peru and Bolivia, and travels to west Africa on private jets, fishing boats and freighters along the notorious "Highway 10" — the shortest route between the continents along the 10th parallel of latitude.

Now the role of al-Qaida-linked Islamists – who controlled northern Mali from early 2012 until they were ousted by French and African troops this year – is fuelling fears for the potential of the drug trade to destabilise the region.

"There is hard evidence of the link between al-Qaida and cocaine trafficking in the Sahara," said Dr Kwesi Aning, director of academic affairs and research at the Kofi Annan international peacekeeping training centre in Ghana. "In the beginning, the trade was mainly dominated by Tuaregs and middlemen who guided traffickers to water and fuel dumps in the desert. But after al-Qaida got involved around 10 years ago, we saw a massive increase in the quantities of cocaine involved. They had the networks, and they had the logistical know-how."

Experts say the lack of law enforcement in the Sahara has allowed both Islamism and the cocaine trade to flourish, with vast, inhospitable, mountainous desert borders all but impossible to police. Many in Mali also accuse successive regimes of the now ousted president Amadou Toumani Touré of being deeply complicit in the trade.

The region's lawlessness was blamed for the 2009 "Air Cocaine" incident, when a Boeing 727 believed to have been carrying up to 10 tonnes of cocaine was found burnt-out in the Malian desert. In 2010, a Malian police commissioner was convicted in connection with attempts to build an airstrip in the desert for future landings. And in the same year, the UK Serious Organised Crime Agency reported that a plane from Venezuela had landed in Mali, and that its cargo was driven by 4x4 vehicles to Timbuktu before authorities lost track of the convoy.

"You have to bear in mind that we are talking about the middle of nowhere," said Pierre Lapaque, representative of the United Nations office on drugs and crime (UNODC) regional office for west and central Africa. "It's a huge piece of sand where you can easily cross borders without knowing it. It is a serious challenge for law enforcement.

"On top of that, these are countries where law enforcement officers are poorly trained, poorly equipped and corrupt, and were logistics don't work. Put that together, and it's a nice opportunity for criminals," he added.

The Nigerian former president Olusegun Obasanjo, commissioner for the recently formed West Africa Commission on Drugs, said: "These criminal groups have the money to buy influence, which makes it difficult to apprehend them. It is affecting the normal operations of civil, military and paramilitary officials. [Drug traffickers] are even paying for political campaigns."

Mohamed said traffickers were highly organised and had well-established means of making their presence even harder to detect. "We waited to collect the drugs at a place between the mountains in the desert called 'al-Hanq' he explained. "The drugs were transported there by camels which travelled across the desert without a guide. The camels were trained by being starved and taken through the same route repeatedly, and fed when they arrive at al-Hanq, until they learned to do the journey alone.

"We would continue in convoys of 4x4s, but we had ways of hiding," Mohamed added. "A reconnaissance vehicle would always go ahead, with no drugs on board, and alert us to any obstacles. We would put grease on the car and stick sand on it as a camouflage, that way it's impossible to see from a distance in the desert."

Lapaque said: "We have heard about camels being trained to carry drugs. These are criminal groups which are well organised, and you have to understand that they have a business approach. They are weighing the potential risks against profits, which are really huge."

Mohamed said he had learned the risks first hand, and has now left the business after his convoy was attacked by heavily armed bandits. "We had stopped to repair a problem with the car, when a car mounted with weapons opened fire on us," he said. "I ran three hundred metres on foot until the shooting stopped, but three of my colleagues and all the attackers were killed. Two vehicles were burnt completely. It scared me so much, I told my boss I didn't want to be involved any more."

Mohamed said his boss is now a senior figure in the drug trade, with a mansion in the Nigerien capital, Niamey. In Timbuktu, the presence of drug chiefs is an open secret, he says, although many were forced to flee during the war.

"Everyone knows who in Timbuktu is doing drug trafficking, even the government," Mohamed said. "When senior officials [in the last government] came to Timbuktu, the drug traffickers were the ones who provided them with 36 brand new 4x4s."

• This article was amended on Friday 3 May 2013. In the original story we misspelled Colombia. This has been corrected.